Reliable DNA signal relay by hairpin structure in DNA-based logic circuit

Abstract

DNA-based logic circuits have received a lot of attention due to their ability to perform basic conventional computations. However, complex DNA circuits still cannot perform in the manner similar to that of complex electronic circuits due to large leakage of signal transmission between circuit components. We introduce a method that can significantly reduce data transmission leakage between two logic gates which increases signal quality within circuits. Our concept is called "separator system" using a DNA hairpin structure and a separator DNA strand which can break the hairpin structure based on the kinetics of DNA branch migration. By placing a toehold of input data for a downstream logic gate in the stem region of the hairpin, the data signal for the next input operation could be held until the hairpin structure is broken, allowing the signal transfer quality between circuit components to be improved. The timing of putting the separator strand in the system could then be used to manage the timing of circuit operations rather proficiently. In this work, we study the functional length of the stem and loop region of the hairpin loop to understand the performance of our separator system on the release of the DNA input data to interact with the subsequent gates in the circuit. We demonstrate the feasibility of our concept by embedding DNA input data into the hairpin structure which resists dynamic DNA strand detachment. This system can be applied to most enzyme-free DNA-based circuits to improve circuit efficiency during the cascading operations.